北京生物医学工程

NetRD: 一种利用Bing搜索结果补充文献挖掘证据集的工具

NetRD: a tool to supplement evidence sentence set by literature mining with Bing data

作者：邹熊峰郑浩然

单位：中国科学技术大学计算机科学与技术学院(合肥 230027)

关键词：生物文献挖掘； Bing web search API；证据集；生物实体关联对；证据补充

分类号：R318

出版年·卷·期（页码）：2019·38·4（377-383）

摘要：

目的当前生物文献挖掘工作的重心是改进各挖掘模块性能，以提升挖掘结果的可信度，但有很大比例的挖掘结果其文献证据很少，为此本文提出一个利用Bing搜索引擎从海量web数据中为文献挖掘得到的生物实体关联对提供补充证据的工具系统。方法利用现有文本挖掘技术从PubMed文献中挖掘一批生物实体关联对，引入Bing web搜索模块，以生物实体名作为关键词从web中利用Bing开放搜索API得到一批搜索结果，将这些结果整理成新的数据源，最终从该新的数据源中挖掘得到一批来自web的补充证据。结果本系统（http://bioinfo.ustc.edu.cn/NetRD）对文献证据较少的生物实体关联对提供了有效的补充证据支持，丰富了文献挖掘结果最终的证据集。结论以web数据作为补充数据源，能够有效地为文献证据很少的生物实体对提供证据补充，为相关研究者确认两个生物实体之间的关联提供重要参考。

Objective The current focus of biological literature mining is to improve the performance of each mining module to enhance the confidence of mining results. However, there are a large proportion of results having few evidence sentences from literature. To alleviate this problem, we propose a tool system which uses Bing search engine to provide additional evidence for the association of biological entities obtained from massive amounts of web data. Methods Firstly, existing bio-literature mining tools are applied to mine a batch of associations between bio-entities. Then, by applying Bing web search API to text mining system, we use biomedical entities as keywords to search from web and fetch the returned results. These results are then collected as another data source. Finally, we mine associations between biomedical entities from the new data source and collect a considerable amount of supplemental evidence sentences from web. Results NetRD (http://bioinfo.ustc.edu.cn/NetRD) provides an effective supplemental evidence support for disease-related genes that have few evidences from literature, and enriches the final set of evidence sentences for literature mining. Conclusions Using Bing search results, NetRD can effectively provide supplemental evidence support for associations between bio-entities with few evidence sentences mined from literature, which is of great reference value for the relevant researchers to confirm whether a bio-entity is associated with another bio-entity.

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